Variant report

Variant	nsv969739
Chromosome Location	chr9:73318954-73369474
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BACH1	chr9:73368475-73368481	H1-hESC	embryonic stem cell:	n/a	n/a
2	CEBPB	chr9:73357619-73357834	HepG2	liver:	n/a	chr9:73357693-73357704
3	CEBPB	chr9:73357607-73357810	A549	lung:	n/a	chr9:73357693-73357704
4	CEBPB	chr9:73357563-73357733	IMR90	lung:	n/a	chr9:73357693-73357704
5	CEBPB	chr9:73361662-73361969	HepG2	liver:	n/a	chr9:73361819-73361832 chr9:73361819-73361830 chr9:73361821-73361832 chr9:73361821-73361830
6	CEBPB	chr9:73361705-73361987	MCF-7	breast:	n/a	chr9:73361819-73361832 chr9:73361819-73361830 chr9:73361821-73361832 chr9:73361821-73361830
7	CEBPB	chr9:73361667-73361979	Hela-S3	cervix:	n/a	chr9:73361819-73361832 chr9:73361819-73361830 chr9:73361821-73361832 chr9:73361821-73361830
8	CEBPB	chr9:73361709-73361869	IMR90	lung:	n/a	chr9:73361819-73361832 chr9:73361819-73361830 chr9:73361821-73361832 chr9:73361821-73361830
9	CTCF	chr9:73345802-73345917	MCF-7	breast:	n/a	chr9:73345846-73345859 chr9:73345844-73345862
10	CTCF	chr9:73348804-73348820	LNCaP	prostate:	n/a	n/a
11	CTCF	chr9:73343196-73343258	GM20000	blood:	n/a	n/a
12	CTCF	chr9:73337632-73337648	GM10248	blood:	n/a	n/a
13	CTCF	chr9:73345821-73345929	MCF-7	breast:	n/a	chr9:73345846-73345859 chr9:73345844-73345862
14	CTCF	chr9:73320209-73320318	LNCaP	prostate:	n/a	n/a
15	CTCF	chr9:73345828-73345899	MCF-7	breast:	n/a	chr9:73345846-73345859 chr9:73345844-73345862
16	CTCF	chr9:73345832-73345884	MCF-7	breast:	n/a	chr9:73345846-73345859 chr9:73345844-73345862
17	CTCF	chr9:73320426-73320489	GM10248	blood:	n/a	n/a
18	CTCF	chr9:73354392-73354442	Spleen_OC	spleen:	n/a	n/a
19	CTCF	chr9:73351044-73351099	Lung_OC	lung:	n/a	n/a
20	CTCF	chr9:73327863-73327919	MCF-7	breast:	n/a	n/a
21	CTCF	chr9:73327847-73327912	MCF-7	breast:	n/a	chr9:73327853-73327866 chr9:73327851-73327869
22	CTCF	chr9:73327817-73327936	MCF-7	breast:	n/a	chr9:73327853-73327866 chr9:73327851-73327869
23	CTCF	chr9:73327826-73327940	MCF-7	breast:	n/a	chr9:73327853-73327866 chr9:73327851-73327869
24	CTCF	chr9:73349090-73349180	LNCaP	prostate:	n/a	n/a
25	CTCF	chr9:73327804-73327871	HepG2	liver:	n/a	chr9:73327853-73327866 chr9:73327851-73327869
26	EP300	chr9:73368200-73368562	SK-N-SH_RA	brain:	n/a	chr9:73368396-73368405
27	EP300	chr9:73368287-73368511	SK-N-SH_RA	brain:	n/a	chr9:73368396-73368405
28	FOS	chr9:73362324-73362459	MCF10A-Er-Src	breast:	n/a	n/a
29	FOXA1	chr9:73321627-73322034	HepG2	liver:	n/a	n/a
30	FOXA1	chr9:73339620-73340027	HepG2	liver:	n/a	n/a
31	FOXP2	chr9:73361700-73361944	SK-N-MC	brain:	n/a	n/a
32	KAP1	chr9:73360570-73362908	U2OS	brain:	n/a	n/a
33	KAP1	chr9:73360846-73362894	HEK293	kidney:	n/a	n/a
34	MAFF	chr9:73359288-73359474	HepG2	liver:	n/a	n/a
35	MAFK	chr9:73359245-73359499	HepG2	liver:	n/a	n/a
36	MAFK	chr9:73359225-73359468	HepG2	liver:	n/a	n/a
37	MYC	chr9:73361724-73361916	MCF10A-Er-Src	breast:	n/a	n/a
38	MYC	chr9:73362227-73362474	MCF10A-Er-Src	breast:	n/a	n/a
39	MYC	chr9:73364505-73364661	MCF10A-Er-Src	breast:	n/a	n/a
40	POLR2A	chr9:73348789-73348850	Gliobla	brain:	n/a	n/a
41	POLR2A	chr9:73361715-73362219	SK-N-MC	brain:	n/a	n/a
42	POLR2A	chr9:73326055-73326197	GM12878	blood:	n/a	n/a
43	POLR2A	chr9:73359657-73359697	GM12878	blood:	n/a	n/a
44	POLR2A	chr9:73321725-73321807	GM12878	blood:	n/a	n/a
45	POLR2A	chr9:73348727-73348755	Gliobla	brain:	n/a	n/a
46	POLR2A	chr9:73367812-73367882	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr9:73344048-73344183	GM12878	blood:	n/a	n/a
48	SP1	chr9:73321652-73321958	HepG2	liver:	n/a	n/a
49	SP1	chr9:73339645-73339951	HepG2	liver:	n/a	n/a
50	SPI1	chr9:73335028-73335210	GM12878	blood:	n/a	chr9:73335127-73335140 chr9:73335128-73335137 chr9:73335126-73335139

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SMC5-2	chr9:73345622-73345772	ENSG00000223966.1
2	lnc-SMC5-2	chr9:73340956-73341141	ENSG00000223966.1
3	lnc-SMC5-1	chr9:73327629-73327779	ENSG00000232086.1
4	lnc-SMC5-1	chr9:73322963-73323148	ENSG00000232086.1

Variant related genes	Relation type
ENSG00000223966	TF binding region
ENSG00000232086	TF binding region

Extended variants
information (count: 621 )
Associated
traits (count: 58 )

Variant overlapped rSNPs/rCNVs (count:621 , 50 per page) page: 1 2 3 4 5 6 7 ... 13

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs62543355	chr9:73320486-73320487	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs62543765	chr9:73327766-73327767	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
3	rs140044698	chr9:73352811-73352812	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs182106963	chr9:73352819-73352820	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs374847482	chr9:73352842-73352843	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs375664034	chr9:73352894-73352895	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs13292536	chr9:73352912-73352913	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs142565633	chr9:73352918-73352919	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs535829808	chr9:73352971-73352972	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs576959850	chr9:73352983-73352984	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs150526623	chr9:73353022-73353023	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs553380140	chr9:73353057-73353058	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs574750553	chr9:73353113-73353114	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs542060209	chr9:73353132-73353133	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs563595608	chr9:73353144-73353145	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs530687995	chr9:73353189-73353190	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs546052555	chr9:73353204-73353205	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs139480082	chr9:73353217-73353218	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs11531868	chr9:73353238-73353239	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs546266661	chr9:73353326-73353327	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs79673604	chr9:73353331-73353332	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs569441968	chr9:73353386-73353387	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs568009862	chr9:73353395-73353396	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs112390808	chr9:73353460-73353461	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs548447385	chr9:73353521-73353522	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs576384133	chr9:73353526-73353527	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs570030928	chr9:73353591-73353592	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs537232806	chr9:73353599-73353600	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs558756305	chr9:73353601-73353602	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs538540033	chr9:73353611-73353612	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs185658055	chr9:73353617-73353618	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs544183781	chr9:73353618-73353619	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs535160192	chr9:73353628-73353629	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs553195117	chr9:73353642-73353643	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs188859086	chr9:73353645-73353646	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs541873058	chr9:73353662-73353663	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs557275579	chr9:73353691-73353692	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs575636765	chr9:73353699-73353700	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs34806905	chr9:73353704-73353705	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs564311099	chr9:73353717-73353718	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs528286946	chr9:73353734-73353735	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs9776589	chr9:73353744-73353745	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs181287286	chr9:73353757-73353758	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs149660230	chr9:73353771-73353772	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs552626776	chr9:73353782-73353783	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs550196714	chr9:73353788-73353789	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs572646718	chr9:73353789-73353790	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs114758225	chr9:73353819-73353820	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs531156356	chr9:73353827-73353828	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs561730712	chr9:73353840-73353841	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:58)

Disease	PMID	Source
Breast cancer	17133270	CNVD
Chordoma	18071362	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Chordoma	21602918	CNVD
Renal cell carcinoma	18592004	CNVD
Developmental delay	19490664	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
Medulloblastoma	21979893	CNVD
microdeletion syndrome	16199537	CNVD
Ovarian cancer	21720365	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Cancer	20164919	CNVD
Urothelial carcinoma	21177765	CNVD
Renal cell carcinoma	21668985	CNVD
Autism	22495311	CNVD
Melanoma	18172304	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Melanoma	22183965	CNVD
Cancer	16751803	CNVD
Myelofibrosis	22110671	CNVD
lymphocytic leukemia	21291569	CNVD
Leukemia	17361228	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Glioblastoma	16823260	CNVD
Leukemia	18688285	CNVD
Non-small cell lung cancer	21044232	CNVD
Brain cancer	20823417	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Astrocytoma	17387387	CNVD
Glioblastoma multiforme	21080181	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Renal cell carcinoma	19461508	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Heart disease	21282601	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Lung cancer	18438408	CNVD
small cell lung cancer	20016488	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Acute myeloid leukemia	21251322	CNVD
Hepatocellular carcinoma	16750200	CNVD
Acute myeloid leukemia	20729466	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Breast cancer	17603634	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Oral cancer	21386901	CNVD
Epilepsy	22083797	CNVD
Glioblastoma multiforme	21750150	CNVD
Cancer	21183584	CNVD
Bipolar disorder	18458673	CNVD
Malignant melanoma	17260012	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:73352800-73367600	Weak transcription	Fetal Kidney	kidney
2	chr9:73355400-73356000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
3	chr9:73355600-73357400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:73356000-73364800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr9:73356600-73368800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr9:73356800-73376000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr9:73357400-73358600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:73357800-73362600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:73358600-73365400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:73361000-73362800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr9:73361000-73362800	Enhancers	NHDF-Ad	bronchial
12	chr9:73361000-73363000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr9:73361200-73362600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr9:73361200-73362800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr9:73361200-73364200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr9:73361400-73361600	Enhancers	Ovary	ovary
17	chr9:73361400-73361800	Enhancers	Pancreas	Pancrea
18	chr9:73361400-73362400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr9:73361400-73363400	Enhancers	Muscle Satellite Cultured Cells	--
20	chr9:73361600-73361800	Enhancers	Aorta	Aorta
21	chr9:73361600-73362800	Enhancers	Osteobl	bone
22	chr9:73361600-73369400	Weak transcription	Ovary	ovary
23	chr9:73361800-73365400	Weak transcription	Aorta	Aorta
24	chr9:73362000-73368600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr9:73362600-73362800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr9:73362600-73364600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr9:73362800-73368400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr9:73364600-73365800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr9:73364800-73369200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr9:73365400-73365600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:73365400-73365800	ZNF genes & repeats	Aorta	Aorta
32	chr9:73365600-73365800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr9:73365800-73368200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr9:73365800-73368800	Weak transcription	Aorta	Aorta
35	chr9:73367000-73376600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr9:73367600-73368600	Strong transcription	Fetal Kidney	kidney
37	chr9:73367800-73370200	Weak transcription	Gastric	stomach
38	chr9:73368200-73369000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr9:73368400-73369200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr9:73368600-73369200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr9:73368600-73370200	Weak transcription	Fetal Kidney	kidney
42	chr9:73368800-73369000	ZNF genes & repeats	Aorta	Aorta
43	chr9:73368800-73369200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr9:73368800-73369800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr9:73369000-73370000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr9:73369000-73378000	Weak transcription	Aorta	Aorta
47	chr9:73369200-73374600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr9:73369200-73377000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr9:73369200-73390200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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